Biomedical subjects

Martin Neumann

Publications and source records attributed to Martin Neumann.

11 recordsLinked to original sources

PubMed2026

The machine-learning classifier ALLCatchR2 identifies 20 T-ALL subtypes across cohorts and age groups.

T-cell acute lymphoblastic leukemia (T-ALL) comprises molecularly diverse subtypes, but robust cross-cohort validations and operational gene-expression definitions are lacking. To establish a gene-expression-anchored framework for T-ALL subtyping, we aggregated 2314 transcriptomes (15 cohorts, age: 0.8-90.8 years). An extended unsupervised approach defined 17 main clusters and 3 subclusters in samples with high blast fractions. Supervised analyses added an overarching immature T-ALL (early T cell precursor [ETP]-like) definition and resolved the LMO2 γδ-like subtype. All clusters contained samples from at least two cohorts. Characteristic genomic driver enrichments were consistent across cohorts, while gene-expression clusters did not correspond exclusively to single driver events but also reflected developmental origins. A machine-learning classifier based on ALLCatchR, our B-cell acute lymphoblastic leukemia (B-ALL) classifier, identified these 20 transcriptomic subtypes and the immature T-ALL (ETP-like) signature with 0.995-1.0 accuracy in a validation set (n = 203). Testing the classifier on a second hold-out data set (n = 265 samples) showed that 92.7% of predictions matched with corresponding driver alterations. Across all samples, 83.2% of cases received high-confidence predictions, 7.3% candidate predictions, and 9.5% remained unclassified, largely because of low blast fractions. We identified a novel gene-expression cluster markedly enriched (P < 0.001) for clonal hematopoiesis mutations (IDH2 R140Q, DNMT3A) and a stem-/progenitor cell-like gene expression. This novel clonal hematopoiesis-related T-ALL subtype was observed in six cohorts and accounted for 8.9% of adults and 39.5% of patients aged >50 years. We extended ALLCatchR into ALLCatchR2, a free R package that now enables B-/T-lineage separation, gene-expression subtyping, blast estimation, and developmental annotation to harmonize T-ALL classification across studies and clinical contexts.

Journal Article↗

PubMed2026

IDH2 clonal hematopoiesis and IKAROS loss cooperate in a B-ALL subtype after lenalidomide therapy for multiple myeloma.

Lenalidomide, a maintenance treatment in multiple myeloma first-line therapy, increases the risk of secondary malignancies, including B-cell precursor acute lymphoblastic leukemia (B-ALL). We present a comprehensive molecular characterization of 57 patients with lenalidomide-associated B-ALL (LenB-ALL), revealing 3 mutational subgroups: (1) TP53mt (30%); (2) IDH2mt (p.R140Q) (23%); and (3) other, including NRAS/KRASmt. Remarkably, IDH2 R140Q mutations were highly enriched in LenB-ALL compared with those in primary B-ALL (P< .001). Furthermore, IKZF1 intragenic deletions, often subclonal and likely RAG recombinase-mediated, were observed in 54% (7/13) of IDH2mt patients with LenB-ALL. IDH2 mutations were not restricted to the leukemic clone: they persisted during measurable residual disease-negative remission and were identified in lymphoid as well as myeloid cell populations using fluorescence-activated cell sorting and single-cell RNA sequencing. This indicates a preleukemic origin of the IDH2 mutation within the context of clonal hematopoiesis. Transcriptomic and DNA methylation analyses revealed a distinct gene expression profile and a DNA hypermethylation phenotype in IDH2mt LenB-ALL, including IDH2mt-specific as well as lenalidomide-associated features. We propose that lenalidomide promotes the expansion of IDH2-mutated clonal hematopoiesis and, via IKAROS downregulation, induces a maturation arrest at the B-cell precursor stage. Subsequent genetic or epigenetic alterations render leukemogenesis independent of ongoing lenalidomide exposure. All these data define IDH2mt B-ALL as a distinct molecular subtype that is markedly overrepresented after lenalidomide treatment and highlight clonal hematopoiesis as a key contributing factor in the development of LenB-ALL.

Humans↗

PubMed2006

Thermodynamically self-consistent liquid state theories for systems with bounded potentials.

The mean spherical approximation (MSA) can be solved semianalytically for the Gaussian core model (GCM) and yields exactly the same expressions for the energy and the virial equations. Taking advantage of this semianalytical framework, we apply the concept of the self-consistent Ornstein-Zernike approximation (SCOZA) to the GCM: a state-dependent function K is introduced in the MSA closure relation which is determined to enforce thermodynamic consistency between the compressibility route and either the energy or virial route. Utilizing standard thermodynamic relations this leads to two differential equations for the function K that have to be solved numerically. Generalizing our concept we propose an integrodifferential-equation-based formulation of the SCOZA which, although requiring a fully numerical solution, has the advantage that it is no longer restricted to the availability of an analytic solution for a particular system. Rather it can be used for an arbitrary potential and even in combination with other closure relations, such as a modification of the hypernetted chain approximation.

Journal Article↗

PubMed2006

Formation of polymorphic cluster phases for a class of models of purely repulsive soft spheres.

We present results from density functional theory and computer simulations that unambiguously predict the occurrence of first-order freezing transitions for a large class of ultrasoft model systems into cluster crystals. The clusters consist of fully overlapping particles and arise without the existence of attractive forces. The number of particles participating in a cluster scales linearly with density, therefore the crystals feature density-independent lattice constants. Clustering is accompanied by polymorphic bcc-fcc transitions, with fcc being the stable phase at high densities.

Journal Article↗

PubMed2005

Optimized arterial trees supplying hollow organs.

Computer models of arterial trees can be generated from optimization principles using the algorithm of constrained constructive optimization (CCO). Up to now this algorithm could handle only tissue areas of convex shape, without concavities. CCO is now generalized to cope also with non-convex organ shapes, possibly featuring external as well as internal concavities. This allows the modeling of a much larger class of interesting real arterial systems. The concept of a generalized domain-potential was developed to represent arbitrary non-convex shapes mathematically and incorporate them as boundary conditions to optimization. Domain-potentials may be derived from analytical representations as well as from finite element triangulations obtained from organ images. To demonstrate the feasibility of the concept, the optimized growth of an arterial tree model is confined to some part of an elliptical shell, representing the free wall of the left ventricle of the heart.

Algorithms↗

PubMed2005

Error estimation of geometrical data obtained by histomorphometry of oblique vessel sections: a computer model study.

The errors of radius and wall thickness of a single vessel due to oblique sectioning in histomorphometry are expressed as a function of the circular shape factor (CSF) of the section's lumen, assuming cylindrical geometry and the absence of tissue deformation. Using computer model trees generated by constrained constructive optimization, mean errors are estimated for an ensemble of vessel segments. A geometrical exclusion criterion for segments cut too obliquely is defined on the basis of a CSF-cutoff value. It is shown that CSF-values ranging from 0.95 to 0.9 are reasonable choices for a cutoff and lead to mean errors of the same order of magnitude (9.6% [9.3%] to 15.4% [14.8%] for the radius [wall thickness]) as errors due to histological tissue processing.

Animals↗

PubMed2003

Fractal properties of perfusion heterogeneity in optimized arterial trees: a model study.

Regional blood flows in the heart muscle are remarkably heterogeneous. It is very likely that the most important factor for this heterogeneity is the metabolic need of the tissue rather than flow dispersion by the branching network of the coronary vasculature. To model the contribution of tissue needs to the observed flow heterogeneities we use arterial trees generated on the computer by constrained constructive optimization. This method allows to prescribe terminal flows as independent boundary conditions, rather than obtaining these flows by the dispersive effects of the tree structure. We study two specific cases: equal terminal flows (model 1) and terminal flows set proportional to the volumes of Voronoi polyhedra used as a model for blood supply regions of terminal segments (model 2). Model 1 predicts, depending on the number Nterm of end-points, fractal dimensions D of perfusion heterogeneities in the range 1.20 to 1.40 and positively correlated nearest-neighbor regional flows, in good agreement with experimental data of the normal heart. Although model 2 yields reasonable terminal flows well approximated by a lognormal distribution, it fails to predict D and nearest-neighbor correlation coefficients r1 of regional flows under normal physiologic conditions: model 2 gives D = 1.69 +/- 0.02 and r1 = -0.18 +/- 0.03 (n = 5), independent of Nterm and consistent with experimental data observed under coronary stenosis and under the reduction of coronary perfusion pressure. In conclusion, flow heterogeneity can be modeled by terminal positions compatible with an existing tree structure without resorting to the flow-dispersive effects of a specific branching tree model to assign terminal flows.

Animals↗

PubMed2003

Heterogeneous perfusion is a consequence of uniform shear stress in optimized arterial tree models.

Using optimized computer models of arterial trees we demonstrate that flow heterogeneity is a necessary consequence of a uniform shear stress distribution. Model trees are generated and optimized under different modes of boundary conditions. In one mode flow is delivered to the tissue as homogeneously as possible. Although this primary goal can be achieved, resulting shear stresses between blood and the vessel walls show very large spread. In a second mode, models are optimized under the condition of uniform shear stress in all segments which in turn renders flow distribution heterogeneous. Both homogeneous perfusion and uniform shear stress are desirable goals in real arterial trees but each of these goals can only be approached at the expense of the other. While the present paper refers only to optimized models, we assume that this dual relation between the heterogeneities in flow and shear stress may represent a more general principle of vascular systems.

Arteries↗

PubMed2003

Voronoi polyhedra analysis of optimized arterial tree models.

Topological and metric properties of Voronoi polyhedra (VP) generated by the distal end points of terminal segments in arterial tree models grown by the method of constrained constructive optimization (CCO) are analyzed with the aim to characterize the spatial distribution of their supply sites relative to randomly distributed points as a reference model. The distributions of the number Nf of Voronoi cell faces, cell volume V, surface area S, area A of individual cell faces, and asphericity parameter alpha of the CCO models are all significantly different from the ones of random points, whereas the distributions of V, S, and alpha are also significantly different among CCO models optimized for minimum intravascular volume and minimum segment length (p < 0.0001). The distributions of Nf, V, and S of the CCO models are reasonably well approximated by two-parameter gamma distributions. We study scaling of intravascular blood volume and arterial cross-sectional area with the volume of supplied tissue, the latter being represented by the VP of the respective terminal segments. We observe scaling exponents from 1.20 +/- 0.007 to 1.08 +/- 0.005 for intravascular blood volume and 0.77 +/- 0.01 for arterial cross-sectional area. Setting terminal flows proportional to the associated VP volumes during tree construction yields a relative dispersion of terminal flows of 37% and a coefficient of skewness of 1.12.

Algorithms↗

PubMed2002

Microscopic distribution functions, structure, and kinetic energy of liquid and solid neon: quantum Monte Carlo simulations.

We have performed extensive path integral Monte Carlo simulations of liquid and solid neon, in order to derive the kinetic energy as well as the single-particle and pair distribution functions of neon atoms in the condensed phases. From the single-particle distribution function n(r) one can derive the momentum distribution and thus obtain an independent estimate of the kinetic energy. The simulations have been carried out using mostly the semiempirical HFD-C2 pair potential by Aziz et al. [R. A. Aziz, W. J. Meath, and A. R. Allnatt, Chem. Phys. 79, 295 (1983)], but, in a few cases, we have also used the Lennard-Jones potential. The differences between the potentials, as measured by the properties investigated, are not very large, especially when compared with the actual precision of the experimental data. The simulation results have been compared with all the experimental information that is available from neutron scattering. The overall agreement with the experiments is very good.

Journal Article↗

PubMedDate not supplied

The spatial pattern of coronary capillaries in patients with dilated, ischemic, or inflammatory cardiomyopathy.

INTRODUCTION: The goal of the present study was to compare the pattern of coronary capillaries in healthy participants and in patients with end-stage heart failure due to idiopathic dilated cardiomyopathy (DCM), ischemic cardiomyopathy (ICM), or inflammatory cardiomyopathy (InfCM). METHODS: Capillary patterns were studied in histological sections from resected hearts from patients with DCM (n=5), ICM (n=5), or InfCM (n=5) and compared with donor hearts showing no signs of cardiac disease (n=3). Patterns were characterized by the distribution of Voronoi polygon areas, A, associated with the centers of capillary profiles, nearest-neighbor distances, d, intercapillary distances (ICD), as well as by means of the pair correlation function g(r). The coefficient of variation of A, CV, was used to characterize capillary patterns as regular, random, or clustered. RESULTS: CV increased from 30.5% (control) to 33.8% (DCM), 36.6% (ICM), and to 40.3% (InfCM). d was minimal in the control group (16.5+/-4.3 microm) and increased to 18.1+/-5.2 microm in the DCM group and to 20.9+/-6.8 and 20.6+/-6.6 microm in the ICM and InfCM groups, respectively. ICD increased from 25.6+/-7.9 (control) to 28.5+/-9.2 (DCM), 34.4+/-12.2 (ICM), and 33.6+/-12.0 microm (InfCM). In all groups, g(r) was markedly different from random points; in the control and DCM group, g(r) showed a weak but distinct first maximum, characteristic for short-range order in a point pattern. CONCLUSIONS: Our data suggest that, for the patients studied, (1) the pattern of coronary capillaries is not purely random, (2) the regularity of the pattern diminishes from the control to DCM, ICM, and InfCM, and (3) ICD increases, whereas capillary density (CD) decreases, from control to DCM, ICM, and InfCM.

Adult↗